Although the results are encouraging, the limitations of the current analysis and possible improvements must be noted. We noted that when the gene rank score cutoff increased from 2.0 to 2.5, the size of the q-values reversed. This observation might be attributed to overly restricted gene selection given that number of SNPs in genes dropped from 2293 in 47 genes to 210 in only 6 genes. Another limitation is that the use of genes from the addiction/alcoholism array represents hypotheses about important genes, as selected by expert review, rather than selection from empirical association data. We could improve the current approach in the following ways. First, although we included seven datasets in the gene ranking, many additional datasets now exist or will be released in the near future that may be used in multi-species data integration. Additionally, this single GWAS dataset is likely to be underpowered given the recent evidence showing many loci of small effect influence most complex human traits. However, a network or pathway analysis approach to analyze a set of genes might improve power [12].
